Reconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace.

Tissues are highly complicated with spatial heterogeneity in gene expression. However, the cutting-edge single-cell RNA-seq technology eliminates the spatial information of individual cells, which contributes to the characterization of cell identities. Herein, we propose single-cell spatial position associated co-embeddings (scSpace), an integrative method to identify spatially variable cell subpopulations by reconstructing cells onto a pseudo-space with spatial transcriptome references (Visium, STARmap, Slide-seq, etc.). We benchmark scSpace with both simulated and biological datasets, and demonstrate that scSpace can accurately and robustly identify spatially variated cell subpopulations. When employed to reconstruct the spatial architectures of complex tissue such as the brain cortex, the small intestinal villus, the liver lobule, the kidney, the embryonic heart, and others, scSpace shows promising performance on revealing the pairwise cellular spatial association within single-cell data. The application of scSpace in melanoma and COVID-19 exhibits a broad prospect in the discovery of spatial therapeutic markers.

The efficacy and safety of combined chinese herbal medicine and western medicine therapy for COVID-19: a systematic review and meta-analysis.

OBJECTIVE: To systematically review the clinical efficacy and safety of Chinese herbal medicine (CHM) with and without Western medicine (WM) for different severity of COVID-19. METHODS: CNKI, PubMed, Wanfang Database, ClinicalTrails.gov, Embase, ChiCTR and ICTRP were searched from 01 Jan, 2020 to 30 Jun, 2021. Two authors independently assessed all the randomized clinical trials (RCTs) for trial inclusion, data extraction and quality assessment. Meta-analysis was conducted using Review Manager software (RevMan 5.4.1). Evidence was assessed using Grading of Recommendations Assessment, Development, and Evaluation (GRADE). Primary outcomes included total effectiveness rate. Secondary outcomes included improvements in symptom improvement and total adverse event rate. Different severity of COVID-19 patients was assessed in subgroup analysis. This study was registered with INPLASY, INPLASY202210072. RESULTS: 22 high quality RCTs involving 1789 participants were included. There were no trial used CHM alone nor compare placebo or no treatment. Compared with WM, combined CHM and WM (CHM-WM) treatment showed higher total effectiveness rate, lower symptom scores of fever, cough, fatigue, dry throat and pharyngalgia, shorter mean time to viral conversion, better Computerized Tomography (CT) image and blood results, fewer total adverse events and worse conditions (P < 0.05). Subgroup analysis showed that the total effectiveness rate of combined CHM-WM group was significantly higher than WM group, especially for mild and moderate patients. No significant differences in mortality and adverse events were found between combined CHM-WM and WM treatment. No serious adverse events and long-term outcomes were reported. CONCLUSION: Current evidence supported the therapeutic effects and safety of combined CHM-WM treatment on COVID-19, especially for patients with mild and moderate symptoms. Long-term effects of therapy are worthy in further study.

Tracing the cell-type-specific modules of immune responses during COVID-19 progression using scDisProcema.

COVID-19 has caused severe threats to lives and damage to property worldwide. The immunopathology of the disease is of particular concern. Currently, researchers have used gene co-expression networks (GCNs) to deepen the study of molecular mechanisms of immune responses to COVID-19. However, most efforts have not fully explored dynamic changes of cell-type-specific molecular networks in the disease process. This study proposes a GCN construction pipeline named single-cell Disease Progression cellular module analysis (scDisProcema), which can trace dynamic changes of immune system response during disease progression using single-cell data. Here, scDisProcema considers changes in cell fate and expression patterns during disease development, identifying gene modules responsible for different immune cells. The hub genes are screened for each module by the specific expression level and the intercellular connectivity of modules. Based on functional items enriched by each gene module, we elucidate the biological processes of different cells involved in disease development and explain the molecular mechanisms underlying the process of cell depletion or proliferation caused by disease. Compared with traditional WGCNA methods, scDisProcema can make more convenient use of the heterogeneity information provided by scRNA-seq data and has great potential in exploring molecular changes during disease progression and organ development.

Status quo and influencing factors for anxiety, depression, and insomnia among 4 237 nurses in Hunan Province. / 湖南省4 237åæŠ¤å£«ç„¦è™‘ã€æŠ‘éƒã€å¤±çœ çŽ°çŠ¶åŠå½±å“å› ç´ .

OBJECTIVES: Public health emergencies have caused significant psychological burden on nurse and affect their mental health. After the coronavirus disease 2019 pandemic, the nurse's mental health has been paid much attention. This study aims to investigate status and influencing factors for anxiety, depression, and insomnia in nurses during the normalized epidemic period, and to further compare the risk of anxiety, depression, and insomnia among nurses at different levels of hospitals between front-line epidemic nurses and other nurses so as to provide a basis for mental health work, nursing management, and relevant study in hospital. METHODS: A total of 4 237 nurses from all levels of hospitals in Hunan Province participated in the survey in December 2020. A self-designed anonymous questionnaire was used in this study. Anxiety, depression, and insomnia were assessed using Generalized Anxiety Disorder-7 items (GAD-7), Patient Health Questionnaire-9 items (PHQ-9), and Insomnia Severity Index (ISI), respectively. Descriptive statistical analysis was used to evaluate nurses' anxiety, depression, and insomnia; t-test, analysis of variance, and multiple linear stepwise regression analysis were used to analyze the influencing factors of nurses' anxiety, depression, and insomnia. RESULTS: The scores of GAD-7 among 4 237 nurses were 4.44±4.20, with 10.3% of them experienced moderate to severe level anxiety. The scores of PHQ-9 were 6.03±4.76, with 17.5% of them experienced moderate to severe level depressive symptom. The scores of ISI were 8.37±5.42, with 12.3% of them experienced moderate to severe insomnia. There were significant differences in GAD-7, PHQ-9, and ISI scores among different groups of hospital levels, gender, professional title, position, education level, night shifts, and family monthly income (all P<0.05). Marital status, whether to participate in the front-line, and whether to participate in psychology training groups were not associated with anxiety, depression, and insomnia (all P>0.05). Gender, hospital level, professional title, educational background, more night shifts, and family monthly income were the influencing factors for the GAD-7 and PHQ-9 scores. Gender, length of service, position, hospital level, educational background, night shifts in the last year, and family monthly income were the influencing factors for ISI score. CONCLUSIONS: There is no difference in the scores of the GAD-7, PHQ-9, and ISI between nurses whether to participate in the front-line, indicating that series of measures for front-line medical staff are effective in China.Meanwhile, some nurses experienced anxiety, depression, and insomnia, and attention should be paid to nurses with low position, more night shifts, lower-level hospitals, and families with low income. It is recommended that management policies, psychological support, and human resource protection should be given to relieve the pressure and maintain the mental health of nurses. At the same time, it is necessary to make mental health knowledge training as a routine training when responding to public health emergencies.

Multiplexing Methods for Simultaneous Large-Scale Transcriptomic Profiling of Samples at Single-Cell Resolution.

Barcoding technology has greatly improved the throughput of cells and genes detected in single-cell RNA sequencing (scRNA-seq) studies. Recently, increasing studies have paid more attention to the use of this technology to increase the throughput of samples, as it has greatly reduced the processing time, technical batch effects, and library preparation costs, and lowered the per-sample cost. In this review, the various DNA-based barcoding methods for sample multiplexing are focused on, specifically, on the four major barcoding strategies. A detailed comparison of the barcoding methods is also presented, focusing on aspects such as sample/cell throughput and gene detection, and guidelines for choosing the most appropriate barcoding technique according to the personalized requirements are developed. Finally, the critical applications of sample multiplexing and technical challenges in combinatorial labeling, barcoding in vivo, and multimodal tagging at the spatially resolved resolution, as well as, the future prospects of multiplexed scRNA-seq, for example, prioritizing and predicting the severity of coronavirus disease 2019 (COVID-19) in patients of different gender and age are highlighted.

Babaodan controls excessive immune responses and may represent a cytokine-targeted agent suitable for COVID-19 treatment.

It has become evident that the actions of pro-inflammatory cytokines and/or the development of a cytokine storm are responsible for the occurrence of severe COVID-19 during SARS-CoV-2 infection. Although immunomodulatory mechanisms vary among viruses, the activation of multiple TLRs that occurs primarily through the recruitment of adapter proteins such as MyD88 and TRIF contributes to the induction of a cytokine storm. Based on this, controlling the robust production of pro-inflammatory cytokines by macrophages may be applicable as a cellular approach to investigate potential cytokine-targeted therapies against COVID-19. In the current study, we utilized TLR2/MyD88 and TLR3/TRIF co-activated macrophages and evaluated the anti-cytokine storm effect of the traditional Chinese medicine (TCM) formula Babaodan (BBD). An RNA-seq-based transcriptomic approach was used to determine the molecular mode of action. Additionally, we evaluated the anti-inflammatory activity of BBD in vivo using a mouse model of post-viral bacterial infection-induced pneumonia and seven severely ill COVID-19 patients. Our study reveals the protective role of BBD against excessive immune responses in macrophages, where the underlying mechanisms involve the inhibition of the NF-κB and MAPK signaling pathways. In vivo, BBD significantly inhibited the release of IL-6, thus resulting in increased survival rates in mice. Based on limited data, we demonstrated that severely ill COVID-19 patients benefited from BBD treatment due to a reduction in the overproduction of IL-6. In conclusion, our study indicated that BBD controls excessive immune responses and may thus represent a cytokine-targeted agent that could be considered to treating COVID-19.

[Mechanism of Xuanfei Baidu Tang in treatment of COVID-19 based on network pharmacology].

The study aimed to investigate the multi-constituent, multi-target mechanism of Xuanfei Baidu Tang(XFBD) in the treatment of coronavirus disease 2019(COVID-19), through exploring the main ingredients and effective targets of XFBD, as well as analyzing the correlation between XFBD targets and COVID-19. The compounds of each herb in XFBD were collected from TCM-PTD, ETCM, TCMSP and SymMap database. Next, the information of meridian tropisms was collected from Chinese Pharmacopoeia(2015 edition), and the target information of the major constituents of XFBD were obtained from TCM-PTD, ETCM, TCMSP and TargetNet database. Subsequently, the target network model and the major modules were generated by Cytoscape, and the functional enrichment analysis of XFBD targets were completed by DAVID and STRING. As a result, ten of the 13 herbs in XFBD belonged to the lung meridian, and 326 of the 1 224 putative XFBD targets were associated with the disease target of COVID-19, among which 109 targets were enriched in the disease pathways of viral infection and lung injury. The main biological pathways regulated by the key XFBD targets included viral infection, energy metabolism, immunity and inflammation, parasites and bacterial infections. In conclusion, the therapeutic mechanism of XFBD in COVID-19 showed a multi-herb, multi-constituent, multi-target pattern, with lung as the chief targeted organ. By regulating a series of biological pathways closely related to the occurrence and development of diseases, XFBD plays a role in balancing immunity, eliminating inflammation, regulating hepatic and biliary metabolism and recovering energy metabolism balance.